The synthesis of oligonucleotide probes on in situ synthesized arrays, such as by photolithography, can result in a population of incomplete or truncated probe sequences which accompany the probe sequences synthesized at the full desired or intended length (“full-length” probes). The presence of such truncated probe sequences can have a detrimental effect on array performance, especially in arrays requiring enzymatic addressing of the free probe terminus, such as polymerase extension reactions or ligation reactions.
In contrast, oligonucleotide probes immobilized on bead arrays (e.g., Illumina) and other spotted arrays are commonly attached to their substrates via an amine or other functional group synthetically attached to the 5′ end of the probe. In this way, only full-length sequences are immobilized, and truncations or other defects associated with an exposed free 3′ end are reduced or virtually eliminated.